retrospective cohort study in a low-incidence
setting using sparse time-series sampling. J
Infect Dis 216(3):366–374. https://doi.
org/10.1093/infdis/jix298
206. Stimson J, Gardy J, Mathema B, Crudu V,
Cohen T, Colijn C (2019) Beyond the SNP
threshold: identifying outbreak clusters using
inferred transmissions. Mol Biol Evol 36
(3):587–603.
https://doi.org/10.1093/
molbev/msy242
207. Fawzy A, Zschock M, Ewers C, Eisenberg T
(2018) Genotyping methods and molecular
epidemiology of Mycobacterium avium
subsp. paratuberculosis (MAP). Int J Vet Sci
Med 6(2):258–264. https://doi.org/10.
1016/j.ijvsm.2018.08.001
208. Harris KA, Underwood A, Kenna DT,
Brooks A, Kavaliunaite E, Kapatai G,
Tewolde R, Aurora P, Dixon G (2015)
Whole-genome sequencing and epidemiological analysis do not provide evidence for crosstransmission of Mycobacterium abscessus in a
cohort of pediatric cystic fibrosis patients.
Clin Infect Dis 60(7):1007–1016. https://
doi.org/10.1093/cid/ciu967
209. Doyle RM, Rubio M, Dixon G, Hartley J,
Klein N, Coll P, Harris KA (2019) Crosstransmission is not the source of new Mycobacterium abscessus infections in a multiCentre cohort of cystic fibrosis patients. Clin
Infect Dis 70(9):1855–1864. https://doi.
org/10.1093/cid/ciz526
210. Nishiuchi Y, Iwamoto T, Maruyama F (2017)
Infection
sources
of
a
common
non-tuberculous mycobacterial pathogen,
Mycobacterium avium Complex. Front Med
(Lausanne) 4:27. https://doi.org/10.3389/
fmed.2017.00027
211. Kreutzfeldt KM, McAdam PR, Claxton P,
Holmes A, Seagar AL, Laurenson IF,
Fitzgerald JR (2013) Molecular longitudinal
tracking of Mycobacterium abscessus spp. during chronic infection of the human lung.
PLoS One 8(5):e63237. https://doi.org/
10.1371/journal.pone.0063237
212. Schuenemann VJ, Avanzi C, Krause-Kyora B,
Seitz A, Herbig A, Inskip S, Bonazzi M,
Reiter E, Urban C, Dangvard Pedersen D,
Taylor GM, Singh P, Stewart GR,
Veleminsky P, Likovsky J, Marcsik A,
Molnar E, Palfi G, Mariotti V, Riga A, Belcastro MG, Boldsen JL, Nebel A, Mays S, Donoghue HD, Zakrzewski S, Benjak A, Nieselt K,
Cole ST, Krause J (2018) Ancient genomes
reveal a high diversity of Mycobacterium leprae
in medieval Europe. PLoS Pathog 14(5):
e1006997. https://doi.org/10.1371/jour
nal.ppat.1006997
213. Mendum TA, Schuenemann VJ, Roffey S,
Taylor GM, Wu H, Singh P, Tucker K,
Hinds J, Cole ST, Kierzek AM, Nieselt K,
Krause J, Stewart GR (2014) Mycobacterium
leprae genomes from a British medieval leprosy hospital: towards understanding an
ancient epidemic. BMC Genomics 15:270.
https://doi.org/10.1186/1471-2164-15270
214. Vandelannoote K, Meehan CJ, Eddyani M,
Affolabi D, Phanzu DM, Eyangoh S,
Jordaens K, Portaels F, Mangas K,
Seemann T, Marsollier L, Marion E,
Chauty A, Landier J, Fontanet A, Leirs H,
Stinear TP, de Jong BC (2017) Multiple
introductions and recent spread of the
emerging human pathogen Mycobacterium
ulcerans across Africa. Genome Biol Evol 9
(3):414–426.
https://doi.org/10.1093/
gbe/evx003
Mycobacterial ID and Characterization Using WGS
457
setting using sparse time-series sampling. J
Infect Dis 216(3):366–374. https://doi.
org/10.1093/infdis/jix298
206. Stimson J, Gardy J, Mathema B, Crudu V,
Cohen T, Colijn C (2019) Beyond the SNP
threshold: identifying outbreak clusters using
inferred transmissions. Mol Biol Evol 36
(3):587–603.
https://doi.org/10.1093/
molbev/msy242
207. Fawzy A, Zschock M, Ewers C, Eisenberg T
(2018) Genotyping methods and molecular
epidemiology of Mycobacterium avium
subsp. paratuberculosis (MAP). Int J Vet Sci
Med 6(2):258–264. https://doi.org/10.
1016/j.ijvsm.2018.08.001
208. Harris KA, Underwood A, Kenna DT,
Brooks A, Kavaliunaite E, Kapatai G,
Tewolde R, Aurora P, Dixon G (2015)
Whole-genome sequencing and epidemiological analysis do not provide evidence for crosstransmission of Mycobacterium abscessus in a
cohort of pediatric cystic fibrosis patients.
Clin Infect Dis 60(7):1007–1016. https://
doi.org/10.1093/cid/ciu967
209. Doyle RM, Rubio M, Dixon G, Hartley J,
Klein N, Coll P, Harris KA (2019) Crosstransmission is not the source of new Mycobacterium abscessus infections in a multiCentre cohort of cystic fibrosis patients. Clin
Infect Dis 70(9):1855–1864. https://doi.
org/10.1093/cid/ciz526
210. Nishiuchi Y, Iwamoto T, Maruyama F (2017)
Infection
sources
of
a
common
non-tuberculous mycobacterial pathogen,
Mycobacterium avium Complex. Front Med
(Lausanne) 4:27. https://doi.org/10.3389/
fmed.2017.00027
211. Kreutzfeldt KM, McAdam PR, Claxton P,
Holmes A, Seagar AL, Laurenson IF,
Fitzgerald JR (2013) Molecular longitudinal
tracking of Mycobacterium abscessus spp. during chronic infection of the human lung.
PLoS One 8(5):e63237. https://doi.org/
10.1371/journal.pone.0063237
212. Schuenemann VJ, Avanzi C, Krause-Kyora B,
Seitz A, Herbig A, Inskip S, Bonazzi M,
Reiter E, Urban C, Dangvard Pedersen D,
Taylor GM, Singh P, Stewart GR,
Veleminsky P, Likovsky J, Marcsik A,
Molnar E, Palfi G, Mariotti V, Riga A, Belcastro MG, Boldsen JL, Nebel A, Mays S, Donoghue HD, Zakrzewski S, Benjak A, Nieselt K,
Cole ST, Krause J (2018) Ancient genomes
reveal a high diversity of Mycobacterium leprae
in medieval Europe. PLoS Pathog 14(5):
e1006997. https://doi.org/10.1371/jour
nal.ppat.1006997
213. Mendum TA, Schuenemann VJ, Roffey S,
Taylor GM, Wu H, Singh P, Tucker K,
Hinds J, Cole ST, Kierzek AM, Nieselt K,
Krause J, Stewart GR (2014) Mycobacterium
leprae genomes from a British medieval leprosy hospital: towards understanding an
ancient epidemic. BMC Genomics 15:270.
https://doi.org/10.1186/1471-2164-15270
214. Vandelannoote K, Meehan CJ, Eddyani M,
Affolabi D, Phanzu DM, Eyangoh S,
Jordaens K, Portaels F, Mangas K,
Seemann T, Marsollier L, Marion E,
Chauty A, Landier J, Fontanet A, Leirs H,
Stinear TP, de Jong BC (2017) Multiple
introductions and recent spread of the
emerging human pathogen Mycobacterium
ulcerans across Africa. Genome Biol Evol 9
(3):414–426.
https://doi.org/10.1093/
gbe/evx003
Mycobacterial ID and Characterization Using WGS
457